Alignments for a candidate for lacA' in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacA' in Dyella japonica UNC79MFTsu3.2

Align lactose 3-dehydrogenase flavin subunit (EC 1.1.99.13) (characterized)
to candidate N515DRAFT_1321 N515DRAFT_1321 Choline dehydrogenase

Query= metacyc::MONOMER-15712
         (579 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1321
          Length = 565

 Score =  655 bits (1689), Expect = 0.0
 Identities = 325/570 (57%), Positives = 407/570 (71%), Gaps = 9/570 (1%)

Query: 11  KNTYDAIVVGSGITGGIAAKELTEKGLKVLVLERGPMVRHLEDYPTAMLDPWQSKYPQGK 70
           K+ YDAIVVG+G++GG AAKELTEKGLK LVL+RGPMV+H  DYPTAM  PW+   P G 
Sbjct: 4   KHVYDAIVVGTGVSGGWAAKELTEKGLKTLVLDRGPMVKH-GDYPTAMKAPWE--LPYGD 60

Query: 71  LPEA-ELNAHYKVQRRTGYTMTEQTQHFFVRDDEHPYTEENRFDWIRGYHVGGRSLTWGR 129
            P   ++  H    R + Y +T+ T+H+FV D ++PY E   FDW RGYHVGGRSL WGR
Sbjct: 61  EPTRHDIERHPIHTRPSFYGITQSTKHWFVDDIDNPYEETRPFDWFRGYHVGGRSLMWGR 120

Query: 130 QSYRHSPIDFEANAREGIAVDWPIRYEDLAPWYEHVERFIGVSGQAEGLPHFPDGHYQPP 189
           QSYR SP+D EAN +EG+ VDWPIRY+D+APWY++VE FIGVSG  E +P  PDG + PP
Sbjct: 121 QSYRLSPMDLEANGKEGVGVDWPIRYDDIAPWYDYVEHFIGVSGSIEHMPQLPDGDFLPP 180

Query: 190 MELNCVEKAFKARSEARFPERRVTIGRTAHLTDPTEEQLALGRTKCQYRNLCIRGCPFGA 249
           MEL CVEK F+ +   +F  R++ IGRTA+L+ P +   +  R  CQYRNLC+RGCPFGA
Sbjct: 181 MELTCVEKDFRDKIAGKFGGRKLIIGRTANLSAPLKHDKSPQRAPCQYRNLCMRGCPFGA 240

Query: 250 YYSSNSGGLIAAERTGNLVIRPNSIVTELIYDERAGRASGVRILDAETRKDEEFHADVIF 309
           Y+SSNS  L AAE+TGN+ +  N+IV ELIYD   G+A+GVR+LDAET    E+ A VIF
Sbjct: 241 YFSSNSSTLPAAEKTGNMTMVTNAIVYELIYDNDKGKATGVRVLDAETGHQTEYFAKVIF 300

Query: 310 LCASALNSAWIMMNSTSSRFPNGFGNASDQLGRNVMDHHLGAGATGQAPEFADMYFSGRR 369
           +CAS   S  I++NSTSSRFPNGFGN S +LG N+MDH  G+GA      + D Y+SGRR
Sbjct: 301 MCASTFGSTHILLNSTSSRFPNGFGNDSGELGHNIMDHLFGSGARAMVDGYDDRYYSGRR 360

Query: 370 PNGIYVPRFRNLGDAASKRSDYLRGFGYQGGAGRATWERDRGQGGRGFGAARKAALSQPG 429
           PNG Y+PR+RN+G   S +S +LRG+GYQGGA R  W   R       G   K A   PG
Sbjct: 361 PNGFYIPRYRNVG---SDKSSFLRGYGYQGGASRQDW--TRLVNTPLIGGDLKRAAQTPG 415

Query: 430 PWTMGLSGFGEMLPYADNRVTLNRDVEDKFGLPTLTMNVTMRDNEMAMRRDMQAAAAEML 489
           PW++ + GFGEMLP   N+VTL+R+ +DK+GLP L  +    +NE+A+ + +   A EM+
Sbjct: 416 PWSISMMGFGEMLPSHRNKVTLDRNRKDKYGLPVLNFDAAHEENELAIGKAIVDDALEMM 475

Query: 490 EAAGFQNVRAHDNGFAPGLGIHEMGTARMGRDPKTSVLNAHNQVHECKNVYVTDGAAMAS 549
            AAG+++VR+       G GIHEMGTARMGRDPKTSVLN  NQ+H CKNVYVTDG+ MAS
Sbjct: 476 SAAGYRDVRSFKVQANVGAGIHEMGTARMGRDPKTSVLNGWNQMHACKNVYVTDGSFMAS 535

Query: 550 ASCVNPSLTYMALTARAADHAVRARKRGEL 579
           + C NPSLTYMA+TARAA HAV   KRG +
Sbjct: 536 SGCQNPSLTYMAMTARAASHAVEELKRGNI 565


Lambda     K      H
   0.319    0.135    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 989
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 579
Length of database: 565
Length adjustment: 36
Effective length of query: 543
Effective length of database: 529
Effective search space:   287247
Effective search space used:   287247
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources